data_93D # _chem_comp.id 93D _chem_comp.name "(1R)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H15 N4 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-03-31 _chem_comp.pdbx_modified_date 2018-03-02 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 306.212 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 93D _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 5VBS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal 93D P P1 P 0 1 N N N 28.755 -6.311 21.467 4.206 0.883 0.146 P 93D 1 93D OP2 O1 O 0 1 N Y N 29.584 -6.000 22.661 4.742 1.582 1.493 OP2 93D 2 93D "O5'" O2 O 0 1 N N N 27.424 -5.506 21.757 2.840 0.090 0.460 "O5'" 93D 3 93D "C5'" C1 C 0 1 N N N 27.548 -4.080 21.847 2.171 -0.722 -0.507 "C5'" 93D 4 93D "C4'" C2 C 0 1 N N R 26.246 -3.473 21.405 0.912 -1.327 0.117 "C4'" 93D 5 93D "C3'" C3 C 0 1 N N S 25.078 -4.298 21.937 0.240 -2.307 -0.870 "C3'" 93D 6 93D "O3'" O3 O 0 1 N N N 24.191 -3.419 22.630 0.602 -3.655 -0.562 "O3'" 93D 7 93D "C2'" C4 C 0 1 N N N 24.544 -4.961 20.675 -1.273 -2.088 -0.645 "C2'" 93D 8 93D "C1'" C5 C 0 1 N N R 24.783 -3.878 19.645 -1.336 -1.002 0.451 "C1'" 93D 9 93D "O4'" O4 O 0 1 N N N 26.106 -3.462 19.955 -0.077 -0.301 0.349 "O4'" 93D 10 93D C1 C6 C 0 1 Y N N 24.752 -4.341 18.241 -2.483 -0.060 0.191 C1 93D 11 93D C6 C7 C 0 1 Y N N 25.209 -5.538 17.838 -2.297 1.094 -0.545 C6 93D 12 93D N5 N1 N 0 1 Y N N 25.172 -5.977 16.413 -3.326 1.901 -0.757 N5 93D 13 93D C4 C8 C 0 1 Y N N 24.568 -4.941 15.509 -4.526 1.615 -0.273 C4 93D 14 93D N3 N2 N 0 1 Y N N 24.132 -3.768 15.992 -4.746 0.520 0.438 N3 93D 15 93D C2 C9 C 0 1 Y N N 24.238 -3.518 17.309 -3.760 -0.337 0.684 C2 93D 16 93D N2 N3 N 0 1 N N N 23.766 -2.300 17.710 -3.993 -1.482 1.427 N2 93D 17 93D N4 N4 N 0 1 N N N 24.453 -5.172 14.160 -5.574 2.487 -0.511 N4 93D 18 93D OP3 O5 O 0 1 N Y N 28.518 -7.729 21.061 3.927 2.010 -0.970 OP3 93D 19 93D HOP2 H1 H 0 0 N Y N 29.633 -5.058 22.776 5.563 2.079 1.378 HOP2 93D 20 93D H2 H2 H 0 1 N N N 28.362 -3.734 21.194 1.893 -0.110 -1.365 H2 93D 21 93D H3 H3 H 0 1 N N N 27.762 -3.789 22.886 2.836 -1.522 -0.832 H3 93D 22 93D H4 H4 H 0 1 N N N 26.170 -2.448 21.798 1.159 -1.836 1.049 H4 93D 23 93D H5 H5 H 0 1 N N N 25.463 -5.072 22.617 0.515 -2.064 -1.896 H5 93D 24 93D H6 H6 H 0 1 N N N 24.628 -3.066 23.396 0.208 -4.313 -1.151 H6 93D 25 93D H7 H7 H 0 1 N N N 23.474 -5.199 20.768 -1.747 -1.735 -1.561 H7 93D 26 93D H8 H8 H 0 1 N N N 25.104 -5.877 20.434 -1.745 -3.009 -0.301 H8 93D 27 93D H9 H9 H 0 1 N N N 24.064 -3.058 19.792 -1.436 -1.460 1.435 H9 93D 28 93D H10 H10 H 0 1 N N N 25.620 -6.210 18.576 -1.323 1.336 -0.944 H10 93D 29 93D H11 H11 H 0 1 N N N 23.415 -1.801 16.918 -4.881 -1.664 1.773 H11 93D 30 93D H12 H12 H 0 1 N N N 23.030 -2.430 18.374 -3.268 -2.103 1.603 H12 93D 31 93D H13 H13 H 0 1 N N N 24.035 -4.377 13.720 -6.457 2.292 -0.158 H13 93D 32 93D H14 H14 H 0 1 N N N 25.360 -5.330 13.770 -5.426 3.293 -1.030 H14 93D 33 93D HOP3 H15 H 0 0 N Y N 29.351 -8.157 20.902 3.269 2.668 -0.708 HOP3 93D 34 93D OP1 OP1 O 0 1 N N N ? ? ? 5.224 -0.067 -0.355 OP1 93D 35 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 93D N4 C4 SING N N 1 93D C4 N3 DOUB Y N 2 93D C4 N5 SING Y N 3 93D N3 C2 SING Y N 4 93D N5 C6 DOUB Y N 5 93D C2 N2 SING N N 6 93D C2 C1 DOUB Y N 7 93D C6 C1 SING Y N 8 93D C1 "C1'" SING N N 9 93D "C1'" "O4'" SING N N 10 93D "C1'" "C2'" SING N N 11 93D "O4'" "C4'" SING N N 12 93D "C2'" "C3'" SING N N 13 93D OP3 P SING N N 14 93D "C4'" "C5'" SING N N 15 93D "C4'" "C3'" SING N N 16 93D P "O5'" SING N N 17 93D P OP2 SING N N 18 93D "O5'" "C5'" SING N N 19 93D "C3'" "O3'" SING N N 20 93D OP2 HOP2 SING N N 21 93D "C5'" H2 SING N N 22 93D "C5'" H3 SING N N 23 93D "C4'" H4 SING N N 24 93D "C3'" H5 SING N N 25 93D "O3'" H6 SING N N 26 93D "C2'" H7 SING N N 27 93D "C2'" H8 SING N N 28 93D "C1'" H9 SING N N 29 93D C6 H10 SING N N 30 93D N2 H11 SING N N 31 93D N2 H12 SING N N 32 93D N4 H13 SING N N 33 93D N4 H14 SING N N 34 93D OP3 HOP3 SING N N 35 93D P OP1 DOUB N N 36 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor 93D SMILES ACDLabs 12.01 "P(OCC1C(O)CC(O1)c2cnc(nc2N)N)(O)(=O)O" 93D InChI InChI 1.03 "InChI=1S/C9H15N4O6P/c10-8-4(2-12-9(11)13-8)6-1-5(14)7(19-6)3-18-20(15,16)17/h2,5-7,14H,1,3H2,(H2,15,16,17)(H4,10,11,12,13)/t5-,6+,7+/m0/s1" 93D InChIKey InChI 1.03 MXGZIYVRSFKADT-RRKCRQDMSA-N 93D SMILES_CANONICAL CACTVS 3.385 "Nc1ncc([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)c(N)n1" 93D SMILES CACTVS 3.385 "Nc1ncc([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)c(N)n1" 93D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(n1)N)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 93D SMILES "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(n1)N)N)C2CC(C(O2)COP(=O)(O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 93D "SYSTEMATIC NAME" ACDLabs 12.01 "(1R)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol" 93D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2,4-bis(azanyl)pyrimidin-5-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 93D "Create component" 2017-03-31 RCSB 93D "Initial release" 2018-03-07 RCSB #